A unique binding mode enables MCM2 to chaperone histones H3–H4 at replication forks

Abstract

During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase, chaperones histones H3–H4. Our first structure shows an H3–H4 tetramer bound by two MCM2 histone-binding domains (HBDs), which hijack interaction sites used by nucleosomal DNA. Our second structure reveals MCM2 and ASF1 cochaperoning an H3–H4 dimer. Mutational analyses show that the MCM2 HBD is required for MCM2–7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3–H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling histones genome wide during DNA replication.

Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation

“…26 and 27). Additionally, threading 3′ DNA into the N-tier places the N-terminal Mcm2 histone binding motif in front of the fork, where it may interact with a parental H3-H4 tetramer (28,29). This new arrangement, with the lagging machinery on top of the fork, may give an advantage to the lagging strand in inheriting parental nucleosomes and their epigenetic marks.…”

DNA Looping Mediates Nucleosome Transfer

“…Although our model does not require specific interactions of histones with the replisome, recent studies have shown that histone H3 may interact with the eukaryotic helicase 45 , providing insight into how replisome progression and histone dynamics may be coordinated 42 . However, the action by which this potential intermediate transfers parental histones to the nascent DNA has yet to be elucidated and is still controversial 46 .…”

Integrated molecular mechanism directing nucleosome reorganization by human FACT

“…In the chromatin-based transcription, the superhelical torsion locally disrupts DNA-histone contacts within the nucleosome (Sheinin et al 2013). In addition, the previous structural reports indicate competitive relationships between the nucleosomal DNA and several histone chaperones, including FACT, during the association with internal histones (Hu et al 2011;Winkler et al 2011;Elsässer et al 2012;Liu et al 2012;Chen et al 2015;Huang et al 2015;Kemble et al 2015;Richet et al 2015). Thus, we assumed that the interaction of hFACT with nucleosomes would involve local detachments of the nucleosomal DNA from histones (Winkler et al 2011;Hsieh et al 2013;Kemble et al 2015).…”

“…Importantly, the hMid-AID/(H3-H4) 2 complex retains the original (H3-H4) 2 subunit structure composed of two copies of an H3-H4 dimer, whereas other histone chaperones disrupt the structure of an H3-H4 tetramer to form complexes with an H3-H4 dimer (English et al 2006;Natsume et al 2007;Hu et al 2011;Elsässer et al 2012;Liu et al 2012). Recently, the crystal structures of the MCM2/(H3-H4) 2 and Spt2/(H3-H4) 2 complexes have been determined Huang et al 2015;Richet et al 2015). These complexes retain the original (H3-H4) 2 structure in the same manner as that of the hMid-AID/(H3-H4) 2 complex.…”